To survive an infection, the body must endure damage from both the pathogen and the immune response to it, a phenomenon called damage tolerance1,2. However, the concept of damage tolerance is not restricted to infections, and can be applied to other diseases as well. The severity of autoimmune disease, for example, depends not only on the magnitude of immune response, but also on the susceptibility of target tissues to the damage caused by that response. The commensal microbiota are becoming increasingly recognized as a determinant of disease severity; therefore, the question arises as to whether the microbiota can determine how much damage we can tolerate. Our central hypothesis is that the microbiota communicate with pathogens, with the immune system and with cellular tolerance and repair mechanisms by means of soluble secreted small molecules, which orchestrate disease susceptibility and severity. Using the nematode Caenorhabditis elegans as a biosensor, we identified indole and several metabolic derivatives as factors secreted by many bacteria, including the commensal microbiota, which may serve this function. We found that brief exposure to indoles activates a signaling pathway in C. elegans that is associated with innate immunity and longevity. Once activated, the animals enter a dauer-like state in which they become resistant to a variety of stressors, a process we term conditioning3. Interestingly, conditioning is evident in mammals as well: exposure to low levels of LPS or even radiation induces a stress response that protects animals from a subsequent exposure to high doses of the stressor that would otherwise prove lethal4. In this proposal, we test the hypothesis that the microbiota acting via indoles, can induce a protective state in organisms as diverse as C. elegans and mammals, using conserved signaling pathways. Conditioning pathways activated by indoles appear to protect the integrity of the intestinal epithelial barrier, and have conserved homologues in Drosophila and mammals. Preliminary data suggest that indoles act via similar pathways to regulate the sensitivity of fly and mammalian intestinal epithelia to damage induced by pathogens, by radiation, or by autoimmune responses (Graft vs. host disease (GvHD)). In Aim 1, we use mutants and RNAi in C. elegans to determine how conditioning can induce protective responses that ensure epithelial barrier integrity, with the goal of identifying conserved pathways in invertebrate and vertebrate systems. In Aim 2, we use knockout mice to test the hypothesis that pathways identified in C. elegans mediate the capacity of indoles to induce tolerance to damage in response to pathogens, environmental stressors (e.g. radiation), or deleterious autoimmune responses. These experiments also have practical medical relevance; we are now developing clinical trials to determine whether administration of indoles, first identified in the bacteria-C. elegans model, can limit susceptibility to GvHD.